DOCSLIB.ORG

Biofilm Composition and Threshold Concentration for Growth Of

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

PUBLIC AND ENVIRONMENTAL HEALTH MICROBIOLOGY crossm Biofilm Composition and Threshold Concentration for Growth of Legionella pneumophila on Surfaces Exposed to Flowing Warm Tap Water without Disinfectant Downloaded from Dick van der Kooij,a Geo L. Bakker,b Ronald Italiaander,a Harm R. Veenendaal,a Bart A. Wullingsa KWR Watercycle Research Institute, Nieuwegein, the Netherlandsa; Vitens NV, Zwolle, the Netherlandsb ABSTRACT Legionella pneumophila in potable water installations poses a potential Received 1 October 2016 Accepted 13 health risk, but quantitative information about its replication in biofilms in relation http://aem.asm.org/ to water quality is scarce. Therefore, biofilm formation on the surfaces of glass and December 2016 Accepted manuscript posted online 6 chlorinated polyvinyl chloride (CPVC) in contact with tap water at 34 to 39°C was in- January 2017 vestigated under controlled hydraulic conditions in a model system inoculated with Citation van der Kooij D, Bakker GL, biofilm-grown L. pneumophila. The biofilm on glass (average steady-state concen- Italiaander R, Veenendaal HR, Wullings BA. tration, 23 Ϯ 9 pg ATP cmϪ2) exposed to treated aerobic groundwater (0.3 mg C 2017. Biofilm composition and threshold concentration for growth of Legionella Ϫ1 ␮ Ϫ1 liter ;1 g assimilable organic carbon [AOC] liter ) did not support growth of the pneumophila on surfaces exposed to flowing organism, which also disappeared from the biofilm on CPVC (49 Ϯ 9 pg ATP cmϪ2) warm tap water without disinfectant. Appl Ϫ2 Environ Microbiol 83:e02737-16. https:// after initial growth. L. pneumophila attained a level of 4.3 log CFU cm in the bio- on February 16, 2017 by guest doi.org/10.1128/AEM.02737-16. films on glass (1,055 Ϯ 225 pg ATP cmϪ2) and CPVC (2,755 Ϯ 460 pg ATP cmϪ2) ex- Editor Johanna Björkroth, University of Helsinki Ϫ1 ␮ Ϫ1 posed to treated anaerobic groundwater (7.9 mg C liter ;10 g AOC liter ). An Copyright © 2017 American Society for elevated biofilm concentration and growth of L. pneumophila were also observed Microbiology. All Rights Reserved. with tap water from the laboratory. The Betaproteobacteria Piscinibacter and Methylo- Address correspondence to Dick van der Kooij, versatilis and amoeba-resisting Alphaproteobacteria predominated in the clones and [email protected]. isolates retrieved from the biofilms. In the biofilms, the Legionella colony count cor- related significantly with the total cell count (TCC), heterotrophic plate count, ATP concentration, and presence of Vermamoeba vermiformis. This amoeba was rarely de- tected at biofilm concentrations of Ͻ100 pg ATP cmϪ2. A threshold concentration of approximately 50 pg ATP cmϪ2 (TCC ϭ 1 ϫ 106 to 2 ϫ 106 cells cmϪ2) was derived for growth of L. pneumophila in biofilms. IMPORTANCE Legionella pneumophila is the etiologic agent in more than 10,000 cases of Legionnaires’ disease that are reported annually worldwide and in most of the drinking water-associated disease outbreaks reported in the United States. The organism proliferates in biofilms on surfaces exposed to warm water in engineered freshwater installations. An investigation with a test system supplied with different types of warm drinking water without disinfectant under controlled hydraulic condi- tions showed that treated aerobic groundwater (0.3 mg literϪ1 of organic carbon) induced a low biofilm concentration that supported no or very limited growth of L. pneumophila. Elevated biofilm concentrations and L. pneumophila colony counts were observed on surfaces exposed to two types of extensively treated groundwa- ter, containing 1.8 and 7.9 mg C literϪ1 and complying with the microbial water quality criteria during distribution. Control measures in warm tap water installations are therefore essential for preventing growth of L. pneumophila. KEYWORDS Legionella pneumophila, predominating biofilm bacteria, threshold biofilm concentration, warm tap water March 2017 Volume 83 Issue 5 e02737-16 Applied and Environmental Microbiology aem.asm.org 1 van der Kooij et al. Applied and Environmental Microbiology egionella pneumophila is the causative agent of Legionnaires’ disease (LD), a life- Lthreatening pneumonia, and proliferates in natural and engineered freshwater systems at warm temperatures. In 2014, the number of annually reported LD cases amounted to more than 6,000 in Europe (1) and more than 5,000 in the United States (2). The wide range of notifications per million inhabitants (Ͻ1 to 39.4) in European countries indicates that the number of reported cases is an underestimation of the true number of cases. Complicated diagnostics and reporting inefficiency are considered the main reasons for these different notification rates (3). The increased number of reported cases in the United States has been attributed to an increasing population of older persons and persons at high risk for infection and to improved diagnostics and reporting (4). More than two thirds of the cases reported in Europe are community acquired, implying that the source of the infection was not identified, with smaller percentages associated with travel (19%), both abroad and domestic, and with health Downloaded from care (8%) (1). In the United States, LD was the most frequently reported drinking water-associated disease from 2009 to 2012 (5, 6). L. pneumophila is detected only incidentally in distributed drinking water in tem- perate regions, but the organism is commonly present in potable water installations in hotels, hospitals, and residential water systems (1, 6–8). L. pneumophila is a nutritionally fastidious organism requiring specific amino acids for growth (9, 10), but a variety of free-living amoebae grazing on biofilms and sediments can serve as hosts and enable http://aem.asm.org/ its proliferation in the aquatic environment (11–16). The optimal growth temperature of L. pneumophila ranges from 37 to 42°C (17, 18), and a warm temperature is essential for its growth because host amoebae digest the bacterium at temperatures of Ͻ20°C (19, 20). Several studies showed that the colony counts of L. pneumophila in potable water installations correlated with the concentrations of organic carbon, iron, manga- nese, and corrosion products in the water (7, 21–23). However, in a recent study, no growth of culturable L. pneumophila was observed in water contained in glass bottles incubated at 32 to 37°C and supplemented with various amounts of ozonated fulvic on February 16, 2017 by guest acid (24). Colony counts of L. pneumophila in water from systems with iron pipes were higher than those in water from systems with pipes of steel and copper (25). Organic polymeric materials used in water installations, e.g., natural and synthetic rubber, polyethylene (cross-linked), polypropylene, and polybutylene, can also promote growth of L. pneumophila (26–31 ). The L. pneumophila colony counts in biofilms on a variety of materials in contact with tap water in experimental systems correlated significantly with the total cell count (TCC) (31) and the ATP level (30) but not with the heterotrophic plate count (HPC) (29). Water temperature management and prevention of stagnation are essential for limiting the growth of L. pneumophila in potable water installations (32–35). Further- more, the use of plumbing materials that do not promote biofilm formation has been advocated (26–29, 36). However, water quality also affects biofilm formation, but the relationship between the concentration of the water-induced biofilm and growth of Legionella is still unclear. Therefore, a test system, the boiler biofilm monitor (BBM), was developed to determine the effects of drinking water without disinfectant on the biofilm formation and growth of L. pneumophila under optimal temperature and hydraulic conditions resembling those in potable water installations (37). This system was tested in the laboratory by using the locally available drinking water and at two groundwater supplies distributing drinking water with either a very low concentration of natural organic matter (NOM) (Ͻ0.5 mg C literϪ1) or a high NOM concentration (7.8 mg C literϪ1). The abundances and identities of Legionella spp. and free-living protozoa in these unchlorinated supplies were reported earlier (38, 39). The objectives of the present study were to (i) assess the relationship between the biofilm concentration and the Legionella colony count in biofilms under controlled conditions in a model system, (ii) identify bacteria predominating in biofilms, (iii) determine the effect of water quality (NOM and assimilable organic carbon [AOC]) on biofilm formation, and (iv) compare the use of glass and chlorinated polyvinyl chloride (CPVC) in the test system. March 2017 Volume 83 Issue 5 e02737-16 aem.asm.org 2 Threshold Biofilm Concentration for Legionella Growth Applied and Environmental Microbiology TABLE 1 Concentrations of total organic carbon (TOC), assimilable organic carbon (AOC), and ATP in the feed water at the test locationsc Water TOC concn AOC concn (␮g acetate % AOC concn after6hat70°C % ATP concn (supply/locationa (mg liter؊1) C equivalents liter؊1) NOXb (␮g acetate C equivalents liter؊1) NOXb (ng liter؊1 Ϯ Ϯ Ϯ Ϯ AT 0.32 0.01 (4) 1.1 0.3 (3) 75 1.9 0.1 (2) 70 0.7 0.6 (13) Ϯ Ϯ Ϯ AD 0.26 0.03 (3) 1.0 0.1 (2) 94 NA NA 0.9 0.7 (13) Ϯ Ϯ Ϯ Ϯ BT 7.9 0.15 (3) 10.9 1.2 (5) 89 22.9 2.8 (5) 94 10.3 2.6 (29) Ϯ Ϯ Ϯ Ϯ BD 7.9 0.16 (3) 8.9 0.7 (1) 90 19.7 3.3 (1) 97 9.6 3.2 (13) Ϯ Ϯ Ϯ Ϯ CD 1.8 0.1 (2) 3.4 0.4 (3) 77 7.9 2.6 (2) 87 3.0 1.4 (14) a AT, groundwater supply A, treated water (T); AD, supply A at a location in the distribution system; BT, supply B, treated water; BD, supply B at a location in the distribution system; CD, groundwater supply C at a location in the distribution system (D).
Recommended publications
  • Toluene Biodegradation in an Algal-Bacterial Airlift Photobioreactor: Influence of the Biomass Concentration and the Presence Of

    Toluene Biodegradation in an Algal-Bacterial Airlift Photobioreactor: Influence of the Biomass Concentration and the Presence Of

    *Manuscript Click here to view linked References 1 Toluene biodegradation in an algal-bacterial airlift 1 2 2 photobioreactor: influence of the biomass concentration and 3 4 3 the presence of an organic phase 5 4 6 7 8 5 Raquel Lebrero*, Roxana Ángeles, Rebeca Pérez, Raúl Muñoz 9 10 11 12 6 Department of Chemical Engineering and Environmental Technology, University of 13 14 7 Valladolid, Dr. Mergelina, s/n, 47011, Valladolid, Spain. Tel. +34 983186424, Fax: 15 8 +34983423013. 16 17 9 18 19 20 10 *Corresponding author: [email protected] 21 22 11 Keywords: Airlift bioreactor, algal-bacterial photobioreactor, toluene biodegradation, 23 24 12 two-phase partitioning bioreactor 25 26 27 13 28 29 14 Abstract 30 31 32 15 The potential of algal-bacterial symbiosis for off-gas abatement was investigated for the first 33 16 time by comparatively evaluating the performance of a bacterial (CB) and an algal-bacterial 34 35 17 (PB) airlift bioreactors during the treatment of a 6 g m-3 toluene laden air emission. The 36 37 18 influence of biomass concentration and of the addition of a non-aqueous phase was also 38 19 investigated. A poor and fluctuating performance was recorded during the initial stages of the 39 40 20 experiment, which was attributed to the low biomass concentration present in both reactors and 41 42 21 to the accumulation of toxic metabolites. In this sense, an increase in the dilution rate from 0.23 43 22 to 0.45 d-1 and in biomass concentration from ~1 to ~5 g L-1 resulted in elimination capacities 44 45 23 (ECs) of 300 g m-3 h-1 (corresponding to removal efficiencies ~ 90 %).
  • Rubisco POSTER 2016 MACUB

    Rubisco POSTER 2016 MACUB

    Direct PCR Detection, Cloning, and Characterization of Bacterial RubisCO Genes from New Jersey Soils Stephanie Zapata*, Anna Gonzalez, Margarita Kulko, Ryan Kim, Theranda Jashari, Aidan Holwerda, Tina Choe, and Luis Jimenez Department of Biology and Horticulture, Bergen Community College, Paramus, New Jersey, USA Abstract Materials and Methods Ribulose-1,5-bisphosphate carboxylase/oxygenase, commonly known by PCR detection of bacterial RubisCO genes in soil the abbreviation RubisCO, is an enzyme involved in the first major step of Cloning libraries carbon fixation, a process by which atmospheric carbon dioxide is The DNA fragments from the PCR amplification of RubisCO converted by bacteria to energy-rich molecules such as glucose. genes were cloned using plasmid pCR®4-TOPO (Life Microbial DNA was extracted from temperate soils using the Zymo Technologies, Thermo Fisher Scientific, Grand Island, NY) Microbe DNA MiniPrep protocol. RubisCo gene sequences were according to the manufacturer’s instructions. Transformations amplified by PCR using degenerate primers cbbLG1F and cbbLG1R. were performed using Mix and Go Competent E. coli strains DNA fragments of approximately 800 base pair were detected in all positive soil samples. Clone libraries were constructed with the amplified (Zymo Research, Irvine, CA). White colonies grown on Luria ç800 bp DNA fragments by ligating the detected fragments with vector pCR®4- Bertani (LB) Agar with ampicillin (50 ug/ml) were transferred to LB TOPO. Transformations were performed using competent Mix and Go broth containing ampicillin (50 ug/ml). Samples were incubated Escherichia coli cells. Plasmids were isolated from each clone using the overnight at 37°C. Zyppy Plasmid Miniprep and inserts were screened by PCR using M13 Plasmids were isolated from each clone using the Zyppy Plasmid DNA primers.
  • Ice-Nucleating Particles Impact the Severity of Precipitations in West Texas

    Ice-Nucleating Particles Impact the Severity of Precipitations in West Texas

    Ice-nucleating particles impact the severity of precipitations in West Texas Hemanth S. K. Vepuri1,*, Cheyanne A. Rodriguez1, Dimitri G. Georgakopoulos4, Dustin Hume2, James Webb2, Greg D. Mayer3, and Naruki Hiranuma1,* 5 1Department of Life, Earth and Environmental Sciences, West Texas A&M University, Canyon, TX, USA 2Office of Information Technology, West Texas A&M University, Canyon, TX, USA 3Department of Environmental Toxicology, Texas Tech University, Lubbock, TX, USA 4Department of Crop Science, Agricultural University of Athens, Athens, Greece 10 *Corresponding authors: [email protected] and [email protected] Supplemental Information 15 S1. Precipitation and Particulate Matter Properties S1.1 Precipitation Categorization In this study, we have segregated our precipitation samples into four different categories, such as (1) snows, (2) hails/thunderstorms, (3) long-lasted rains, and (4) weak rains. For this categorization, we have considered both our observation-based as well as the disdrometer-assigned National Weather Service (NWS) 20 code. Initially, the precipitation samples had been assigned one of the four categories based on our manual observation. In the next step, we have used each NWS code and its occurrence in each precipitation sample to finalize the precipitation category. During this step, a precipitation sample was categorized into snow, only when we identified a snow type NWS code (Snow: S-, S, S+ and/or Snow Grains: SG). Likewise, a precipitation sample was categorized into hail/thunderstorm, only when the cumulative sum of NWS codes for hail was 25 counted more than five times (i.e., A + SP ≥ 5; where A and SP are the codes for soft hail and hail, respectively).
  • The Different Dietary Sugars Modulate The

    The Different Dietary Sugars Modulate The

    Wang et al. BMC Microbiology (2020) 20:61 https://doi.org/10.1186/s12866-020-01726-6 RESEARCH ARTICLE Open Access The different dietary sugars modulate the composition of the gut microbiota in honeybee during overwintering Hongfang Wang, Chunlei Liu, Zhenguo Liu, Ying Wang, Lanting Ma and Baohua Xu* Abstract Background: The health of honeybee colonies is critical for bee products and agricultural production, and colony health is closely associated with the bacteria in the guts of honeybees. Although colony loss in winter is now the primary restriction in beekeeping, the effects of different sugars as winter food on the health of honeybee colonies are not well understood. Therefore, in this study, the influence of different sugar diets on honeybee gut bacteria during overwintering was examined. Results: The bacterial communities in honeybee midguts and hindguts before winter and after bees were fed honey, sucrose, and high-fructose syrup as winter-food were determined by targeting the V3-V4 region of 16S rDNA using the Illumina MiSeq platform. The dominant microbiota in honeybee guts were the phyla Proteobacteria (63.17%), Firmicutes (17.61%; Lactobacillus, 15.91%), Actinobacteria (4.06%; Bifidobacterium, 3.34%), and Bacteroidetes (1.72%). The dominant taxa were conserved and not affected by season, type of overwintering sugar, or spatial position in the gut. However, the relative abundance of the dominant taxa was affected by those factors. In the midgut, microbial diversity of the sucrose group was higher than that of the honey and high-fructose syrup groups, but in the hindgut, microbial diversity of the honey and high-fructose groups was higher than that in the sucrose group.
  • 1 Horizontal Gene Transfer of a Unique Nif Island Drives Convergent Evolution of Free-Living

    1 Horizontal Gene Transfer of a Unique Nif Island Drives Convergent Evolution of Free-Living

    bioRxiv preprint doi: https://doi.org/10.1101/2021.02.03.429501; this version posted February 3, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Horizontal gene transfer of a unique nif island drives convergent evolution of free-living 2 N2-fixing Bradyrhizobium 3 4 Jinjin Tao^, Sishuo Wang^, Tianhua Liao, Haiwei Luo* 5 6 Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of 7 Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 8 9 ^These authors contribute equally to this work. 10 11 *Corresponding author: 12 Haiwei Luo 13 School of Life Sciences, The Chinese University of Hong Kong 14 Shatin, Hong Kong SAR 15 Phone: (+852) 39436121 16 E-mail: [email protected] 17 18 Running Title: Free-living Bradyrhizobium evolution 19 Keywords: free-living Bradyrhizobium, nitrogen fixation, lifestyle, HGT 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.02.03.429501; this version posted February 3, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 20 Summary 21 The alphaproteobacterial genus Bradyrhizobium has been best known as N2-fixing members that 22 nodulate legumes, supported by the nif and nod gene clusters.
  • Characterization of Bacterial Communities Associated

    Characterization of Bacterial Communities Associated

    www.nature.com/scientificreports OPEN Characterization of bacterial communities associated with blood‑fed and starved tropical bed bugs, Cimex hemipterus (F.) (Hemiptera): a high throughput metabarcoding analysis Li Lim & Abdul Hafz Ab Majid* With the development of new metagenomic techniques, the microbial community structure of common bed bugs, Cimex lectularius, is well‑studied, while information regarding the constituents of the bacterial communities associated with tropical bed bugs, Cimex hemipterus, is lacking. In this study, the bacteria communities in the blood‑fed and starved tropical bed bugs were analysed and characterized by amplifying the v3‑v4 hypervariable region of the 16S rRNA gene region, followed by MiSeq Illumina sequencing. Across all samples, Proteobacteria made up more than 99% of the microbial community. An alpha‑proteobacterium Wolbachia and gamma‑proteobacterium, including Dickeya chrysanthemi and Pseudomonas, were the dominant OTUs at the genus level. Although the dominant OTUs of bacterial communities of blood‑fed and starved bed bugs were the same, bacterial genera present in lower numbers were varied. The bacteria load in starved bed bugs was also higher than blood‑fed bed bugs. Cimex hemipterus Fabricus (Hemiptera), also known as tropical bed bugs, is an obligate blood-feeding insect throughout their entire developmental cycle, has made a recent resurgence probably due to increased worldwide travel, climate change, and resistance to insecticides1–3. Distribution of tropical bed bugs is inclined to tropical regions, and infestation usually occurs in human dwellings such as dormitories and hotels 1,2. Bed bugs are a nuisance pest to humans as people that are bitten by this insect may experience allergic reactions, iron defciency, and secondary bacterial infection from bite sores4,5.
  • Phylogenetic and Functional Characterization of Symbiotic Bacteria in Gutless Marine Worms (Annelida, Oligochaeta)

    Phylogenetic and Functional Characterization of Symbiotic Bacteria in Gutless Marine Worms (Annelida, Oligochaeta)

    Phylogenetic and functional characterization of symbiotic bacteria in gutless marine worms (Annelida, Oligochaeta) Dissertation zur Erlangung des Grades eines Doktors der Naturwissenschaften -Dr. rer. nat.- dem Fachbereich Biologie/Chemie der Universität Bremen vorgelegt von Anna Blazejak Oktober 2005 Die vorliegende Arbeit wurde in der Zeit vom März 2002 bis Oktober 2005 am Max-Planck-Institut für Marine Mikrobiologie in Bremen angefertigt. 1. Gutachter: Prof. Dr. Rudolf Amann 2. Gutachter: Prof. Dr. Ulrich Fischer Tag des Promotionskolloquiums: 22. November 2005 Contents Summary ………………………………………………………………………………….… 1 Zusammenfassung ………………………………………………………………………… 2 Part I: Combined Presentation of Results A Introduction .…………………………………………………………………… 4 1 Definition and characteristics of symbiosis ...……………………………………. 4 2 Chemoautotrophic symbioses ..…………………………………………………… 6 2.1 Habitats of chemoautotrophic symbioses .………………………………… 8 2.2 Diversity of hosts harboring chemoautotrophic bacteria ………………… 10 2.2.1 Phylogenetic diversity of chemoautotrophic symbionts …………… 11 3 Symbiotic associations in gutless oligochaetes ………………………………… 13 3.1 Biogeography and phylogeny of the hosts …..……………………………. 13 3.2 The environment …..…………………………………………………………. 14 3.3 Structure of the symbiosis ………..…………………………………………. 16 3.4 Transmission of the symbionts ………..……………………………………. 18 3.5 Molecular characterization of the symbionts …..………………………….. 19 3.6 Function of the symbionts in gutless oligochaetes ..…..…………………. 20 4 Goals of this thesis …….…………………………………………………………..
  • Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights Into the Origin and Distribution of Nitrogen Fixation Across Bacteria and Archaea

    Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights Into the Origin and Distribution of Nitrogen Fixation Across Bacteria and Archaea

    microorganisms Article Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights into the Origin and Distribution of Nitrogen Fixation across Bacteria and Archaea Amrit Koirala 1 and Volker S. Brözel 1,2,* 1 Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA; [email protected] 2 Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0004, South Africa * Correspondence: [email protected]; Tel.: +1-605-688-6144 Abstract: The phylogeny of nitrogenase has only been analyzed using the structural proteins NifHDK. As nifHDKENB has been established as the minimum number of genes necessary for in silico predic- tion of diazotrophy, we present an updated phylogeny of diazotrophs using both structural (NifHDK) and cofactor assembly proteins (NifENB). Annotated Nif sequences were obtained from InterPro from 963 culture-derived genomes. Nif sequences were aligned individually and concatenated to form one NifHDKENB sequence. Phylogenies obtained using PhyML, FastTree, RapidNJ, and ASTRAL from individuals and concatenated protein sequences were compared and analyzed. All six genes were found across the Actinobacteria, Aquificae, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Deferribacteres, Firmicutes, Fusobacteria, Nitrospira, Proteobacteria, PVC group, and Spirochaetes, as well as the Euryarchaeota. The phylogenies of individual Nif proteins were very similar to the overall NifHDKENB phylogeny, indicating the assembly proteins have evolved together. Our higher resolution database upheld the three cluster phylogeny, but revealed undocu- Citation: Koirala, A.; Brözel, V.S. mented horizontal gene transfers across phyla. Only 48% of the 325 genera containing all six nif genes Phylogeny of Nitrogenase Structural and Assembly Components Reveals are currently supported by biochemical evidence of diazotrophy.
  • Monitoring of Bacterial Communities in a Phytoremediation Plant for the Decontamination of Polluted Marine Sediments”

    Monitoring of Bacterial Communities in a Phytoremediation Plant for the Decontamination of Polluted Marine Sediments”

    Research Doctorate School in Biological and Molecular Sciences Cycle XXV “Monitoring of bacterial communities in a phytoremediation plant for the decontamination of polluted marine sediments” Candidate: Carolina Chiellini Supervisors: Dott. Giulio Petroni Prof. Ing. Renato Iannelli 2013 BIO/05 INDEX SUMMARY .......................................................................................................................................................... 1 RIASSUNTO ........................................................................................................................................................ 3 1 INTRODUCTION: AN OVERVIEW ON THE TOPIC ........................................................................... 5 1.1 THE NORMATIVE CONCERNING DREDGED SEDIMENTS ........................................................................ 7 1.1.1 The European scenario ......................................................................................................................... 7 1.1.2 The Italian scenario ................................................................................................................................ 9 1.2 THE PROBLEM OF DREDGED SEDIMENTS ................................................................................................ 12 1.2.1 Types and sources of pollutants in marine sediments .............................................................. 12 1.2.2 How to treat polluted sediments ......................................................................................................

  • Cluster 1 Cluster 3 Cluster 2

    5 9 Luteibacter yeojuensis strain SU11 (Ga0078639_1004, 2640590121) 7 0 Luteibacter rhizovicinus DSM 16549 (Ga0078601_1039, 2631914223) 4 7 Luteibacter sp. UNCMF366Tsu5.1 (FG06DRAFT_scaffold00001.1, 2595447474) 5 5 Dyella japonica UNC79MFTsu3.2 (N515DRAFT_scaffold00003.3, 2558296041) 4 8 100 Rhodanobacter sp. Root179 (Ga0124815_151, 2699823700) 9 4 Rhodanobacter sp. OR87 (RhoOR87DRAFT_scaffold_21.22, 2510416040) Dyella japonica DSM 16301 (Ga0078600_1041, 2640844523) Dyella sp. OK004 (Ga0066746_17, 2609553531) 9 9 9 3 Xanthomonas fuscans (007972314) 100 Xanthomonas axonopodis (078563083) 4 9 Xanthomonas oryzae pv. oryzae KACC10331 (NC_006834, 637633170) 100 100 Xanthomonas albilineans USA048 (Ga0078502_15, 2651125062) 5 6 Xanthomonas translucens XT123 (Ga0113452_1085, 2663222128) 6 5 Lysobacter enzymogenes ATCC 29487 (Ga0111606_103, 2678972498) 100 Rhizobacter sp. Root1221 (056656680) Rhizobacter sp. Root1221 (Ga0102088_103, 2644243628) 100 Aquabacterium sp. NJ1 (052162038) Aquabacterium sp. NJ1 (Ga0077486_101, 2634019136) Uliginosibacterium gangwonense DSM 18521 (B145DRAFT_scaffold_15.16, 2515877853) 9 6 9 7 Derxia lacustris (085315679) 8 7 Derxia gummosa DSM 723 (H566DRAFT_scaffold00003.3, 2529306053) 7 2 Ideonella sp. B508-1 (I73DRAFT_BADL01000387_1.387, 2553574224) Zoogloea sp. LCSB751 (079432982) PHB-accumulating bacterium (PHBDraf_Contig14, 2502333272) Thiobacillus sp. 65-1059 (OJW46643.1) 8 4 Dechloromonas aromatica RCB (NC_007298, 637680051) 8 4 7 7 Dechloromonas sp. JJ (JJ_JJcontig4, 2506671179) Dechloromonas RCB 100 Azoarcus
  • Physiology and Biochemistry of Aromatic Hydrocarbon-Degrading Bacteria That Use Chlorate And/Or Nitrate As Electron Acceptor

    Physiology and Biochemistry of Aromatic Hydrocarbon-Degrading Bacteria That Use Chlorate And/Or Nitrate As Electron Acceptor

    Invitation for the public defense of my thesis Physiology and biochemistry of aromatic hydrocarbon-degrading of aromatic and biochemistry Physiology bacteria that use chlorate and/or nitrate as electron acceptor as electron nitrate and/or use chlorate that bacteria Physiology and biochemistry Physiology and biochemistry of aromatic hydrocarbon-degrading of aromatic hydrocarbon- degrading bacteria that bacteria that use chlorate and/or nitrate as electron acceptor use chlorate and/or nitrate as electron acceptor The public defense of my thesis will take place in the Aula of Wageningen University (Generall Faulkesweg 1, Wageningen) on December 18 2013 at 4:00 pm. This defense is followed by a reception in Café Carré (Vijzelstraat 2, Wageningen). Margreet J. Oosterkamp J. Margreet Paranimphs Ton van Gelder ([email protected]) Aura Widjaja Margreet J. Oosterkamp ([email protected]) Marjet Oosterkamp (911 W Springfield Ave Apt 19, Urbana, IL 61801, USA; [email protected]) Omslag met flap_MJOosterkamp.indd 1 25-11-2013 5:58:31 Physiology and biochemistry of aromatic hydrocarbon-degrading bacteria that use chlorate and/or nitrate as electron acceptor Margreet J. Oosterkamp Thesis-MJOosterkamp.indd 1 25-11-2013 6:42:09 Thesis committee Thesis supervisor Prof. dr. ir. A. J. M. Stams Personal Chair at the Laboratory of Microbiology Wageningen University Thesis co-supervisors Dr. C. M. Plugge Assistant Professor at the Laboratory of Microbiology Wageningen University Dr. P. J. Schaap Assistant Professor at the Laboratory of Systems and Synthetic Biology Wageningen University Other members Prof. dr. L. Dijkhuizen, University of Groningen Prof. dr. H. J. Laanbroek, University of Utrecht Prof.
  • Structure and Evolution of Chlorate Reduction Composite Transposons

    Structure and Evolution of Chlorate Reduction Composite Transposons

    RESEARCH ARTICLE Structure and Evolution of Chlorate Reduction Composite Transposons Iain C. Clark,a Ryan A. Melnyk,b Anna Engelbrektson,b John D. Coatesb Department of Civil and Environmental Engineeringa and Department of Plant and Microbial Biology,b University of California, Berkeley, California, USA ABSTRACT The genes for chlorate reduction in six bacterial strains were analyzed in order to gain insight into the metabolism. A newly isolated chlorate-reducing bacterium (Shewanella algae ACDC) and three previously isolated strains (Ideonella dechlora- tans, Pseudomonas sp. strain PK, and Dechloromarinus chlorophilus NSS) were genome sequenced and compared to published sequences (Alicycliphilus denitrificans BC plasmid pALIDE01 and Pseudomonas chloritidismutans AW-1). De novo assembly of genomes failed to join regions adjacent to genes involved in chlorate reduction, suggesting the presence of repeat regions. Using a bioinformatics approach and finishing PCRs to connect fragmented contigs, we discovered that chlorate reduction genes are flanked by insertion sequences, forming composite transposons in all four newly sequenced strains. These insertion sequences delineate regions with the potential to move horizontally and define a set of genes that may be important for chlorate reduction. In addition to core metabolic components, we have highlighted several such genes through comparative analysis and visualiza- tion. Phylogenetic analysis places chlorate reductase within a functionally diverse clade of type II dimethyl sulfoxide (DMSO) reductases, part of a larger family of enzymes with reactivity toward chlorate. Nucleotide-level forensics of regions surrounding chlorite dismutase (cld), as well as its phylogenetic clustering in a betaproteobacterial Cld clade, indicate that cld has been mobi- lized at least once from a perchlorate reducer to build chlorate respiration.